biobb_dna updated to 4.2.1

bioexcel · Jun 17, 2024 · 2bd5568 · 2bd5568
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 [![](https://readthedocs.org/projects/biobb-wf-md-setup/badge/?version=latest)](https://biobb-wf-dna-helparms.readthedocs.io/en/latest/?badge=latest)
 [![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_dna_helparms/HEAD?labpath=biobb_wf_dna_helparms%2Fnotebooks%2Fbiobb_wf_dna_helparms.ipynb)
-<!--[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_dna_helparms/blob/main/biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynb)-->
+[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_dna_helparms/blob/main/biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynb)
 
 # Structural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb)
 
@@ -40,7 +40,7 @@ Click here to [view tutorial in Read the Docs](https://biobb-wf-dna-helparms.rea
 
 Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_dna_helparms/HEAD?labpath=biobb_wf_dna_helparms%2Fnotebooks%2Fbiobb_wf_dna_helparms.ipynb)
 
-<!--Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_dna_helparms/blob/main/biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynb)-->
+Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_dna_helparms/blob/main/biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynb)
 
 ***
 

diff --git a/binder/environment.yml b/binder/environment.yml
@@ -3,6 +3,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python==3.9
-  - biobb_dna==4.2.0
+  - biobb_dna==4.2.1
   - matplotlib
diff --git a/biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynb b/biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynb
@@ -90,9 +90,7 @@
     "  except FileNotFoundError:\n",
     "    subprocess.run([sys.executable, \"-m\", \"pip\", \"install\", \"condacolab\"], check=True)\n",
     "    import condacolab\n",
-    "    condacolab.install_from_url(\"https://repo.anaconda.com/miniconda/Miniconda3-py39_24.3.0-0-Linux-x86_64.sh\")\n",
-    "    # Remove pinned specs\n",
-    "    subprocess.run([\"mv\", \"/usr/local/conda-meta/pinned\", \"/usr/local/conda-meta/pinned.bk\"], check=True)\n",
+    "    condacolab.install()\n",
     "    # Clone repository\n",
     "    repo_URL = \"https://github.com/bioexcel/biobb_wf_dna_helparms.git\"\n",
     "    repo_name = Path(repo_URL).name.split('.')[0]\n",

diff --git a/conda_env/environment.yml b/conda_env/environment.yml
@@ -3,6 +3,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - biobb_dna==4.2.0
+  - biobb_dna==4.2.1
   - matplotlib
   - jupyter